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- PDB-9c1s: Fab F946 in complex with OspC type A -

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Basic information

Entry
Database: PDB / ID: 9c1s
TitleFab F946 in complex with OspC type A
Components
  • F946 Fab Heavy Chain
  • F946 Fab Light Chain
  • Outer surface protein C
KeywordsIMMUNE SYSTEM/ANTIGEN / Fab-antigen complex / IMMUNE SYSTEM / IMMUNE SYSTEM-ANTIGEN complex
Function / homologyexternal side of cell outer membrane / Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / Outer surface protein C
Function and homology information
Biological speciesHomo sapiens (human)
Borreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00040 United States
CitationJournal: To Be Published
Title: Fab F946 in complex with OspC type A
Authors: Rudolph, M.J. / Mantis, N.
History
DepositionMay 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: F946 Fab Heavy Chain
L: F946 Fab Light Chain
A: F946 Fab Heavy Chain
B: F946 Fab Light Chain
C: Outer surface protein C
D: Outer surface protein C


Theoretical massNumber of molelcules
Total (without water)131,0976
Polymers131,0976
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-106 kcal/mol
Surface area50440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.815, 95.141, 182.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody F946 Fab Heavy Chain


Mass: 24591.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody F946 Fab Light Chain


Mass: 23429.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Outer surface protein C / PC


Mass: 17528.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: ospC, BB_B19 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q07337
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM Ammonium nitrate and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 42767 / % possible obs: 99.9 % / Redundancy: 11.5 % / Biso Wilson estimate: 38.5 Å2 / CC1/2: 0.997 / Net I/σ(I): 10
Reflection shellResolution: 2.55→2.59 Å / Num. unique obs: 1909 / CC1/2: 0.71 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.57 Å / SU ML: 0.3452 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.2688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2508 2083 4.95 %
Rwork0.1958 39993 -
obs0.1985 42076 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8960 0 0 233 9193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029133
X-RAY DIFFRACTIONf_angle_d0.560912382
X-RAY DIFFRACTIONf_chiral_restr0.03991435
X-RAY DIFFRACTIONf_plane_restr0.00391563
X-RAY DIFFRACTIONf_dihedral_angle_d5.18071236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.3305930.25161688X-RAY DIFFRACTION61.5
2.66-2.730.31151300.26212479X-RAY DIFFRACTION92
2.73-2.80.33211310.26692614X-RAY DIFFRACTION95.02
2.8-2.880.32481260.25852632X-RAY DIFFRACTION96.53
2.88-2.970.36271360.25882721X-RAY DIFFRACTION98.82
2.97-3.080.34281250.2422749X-RAY DIFFRACTION99.93
3.08-3.20.30841320.22832768X-RAY DIFFRACTION100
3.2-3.350.27371550.21592727X-RAY DIFFRACTION99.97
3.35-3.530.2651740.21362721X-RAY DIFFRACTION100
3.53-3.750.22611600.19782742X-RAY DIFFRACTION100
3.75-4.040.24631630.17932750X-RAY DIFFRACTION100
4.04-4.440.2351140.15412825X-RAY DIFFRACTION100
4.44-5.080.17741460.14382784X-RAY DIFFRACTION100
5.08-6.40.21141470.17282844X-RAY DIFFRACTION100
6.4-47.570.19741510.17262949X-RAY DIFFRACTION99.01
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.198907071790.290500532780.4214584759893.20600175207-0.1165994377952.4570457573-0.0701084740276-0.102774851047-0.2186969326610.0006447028705960.2358441414280.5339443732840.148266128289-0.263473939688-0.1050149627780.283862828076-0.0278040593550.004664574331650.2337411560060.01345553100050.321665701787-11.66251952096.4344571964222.9382377989
23.588204849241.86794771553-1.139538971193.79637176884-0.1659008623995.197101053570.1641970387020.27523906403-0.366170821353-0.307816143070.106424220058-0.2340962281750.5790609401860.569926053253-0.1302772198090.4134162021340.135781508197-0.1457246957730.371944105753-0.1358863283870.429845675079-9.725322821473.2228355602-10.8487098537
32.44320900943-0.481023308393-0.5800447410723.749502311380.2225112630625.03921489129-0.2496725709980.07078986253870.160660470548-0.006039425972150.2142803943050.394626007574-0.092552144443-0.1953552162450.006694869688470.298630754584-0.0151528818847-0.08006021484060.1998937544090.01748137770060.343789038118-8.9221986319527.153297523216.6916439424
45.302445674351.19849082821-4.571678976250.84996515718-0.4259309820696.275882264570.3261487152690.4819900049410.4700310283880.0412375531265-0.09619720017120.589842439608-1.46194125254-0.416827967258-0.2513574277470.5404135304720.0821270271948-0.06195057507960.217093317367-0.05461626658690.465323470485-9.4039578493533.380073131720.0855324436
55.523731881243.88217795329-3.307855384983.95781319402-3.219498828577.78101229643-0.151267216713-0.01898456403850.170799945098-0.3440379393230.1733037724580.2074567363010.322872693579-0.1242935190320.008700142724160.3495884704870.0692540428544-0.08111342238160.19965341024-0.04577743636360.337496332343-10.507991837623.652756710116.2911578786
61.61946394747-0.3294824606830.6352466538452.723937014463.554158870575.35545164694-0.09339106524340.4891754149580.247169141345-0.6154452958040.827531720345-0.2844982781830.00404444796128-0.195061841482-0.6073856321320.464672636959-0.175634337794-0.03261735322710.4387865102040.04224796542680.240600194512-8.4049401530729.1791014488-5.32261696244
74.673769845061.587929561141.520420493934.61007982220.07831680049973.590683163720.2505892142510.617286332123-0.834518806344-0.24093679260.351605139047-0.4921143596690.4565019647840.361717286419-0.5639007535170.4932607639510.0381113373146-0.03287357798190.507248083956-0.1550467729680.444012954575-17.59818861554.98988448028-21.1480367969
83.735358392850.7936005128571.882096505542.236940176381.223127279392.388534430030.05910423180240.295821020114-0.1183704337290.02696099978930.02049685576210.0636422524585-0.0919268729910.0892470015351-0.04208533817630.310034841203-0.01942105923160.03896464125190.265528250326-0.02060468965810.255429408887-21.28991263717.4822729563-14.4908940234
94.620930368834.134915529252.888990781343.9258477032.260713835722.412953432360.287046384183-0.610774135075-0.340139001803-0.397208286823-0.440216930872-0.714315084499-0.08484617244961.240857396410.06652748550190.439881236666-0.0670937559537-0.01366045094280.511410512382-0.001690223030630.514431568516-5.8993107279221.5841696516-5.73101638356
105.132991813463.913181228442.285972249367.405245885861.771290839876.65388783501-0.174542235810.5140404727770.088678799894-1.00968184077-0.06321064866370.339476957617-0.3079080616020.09559618487690.1938869764330.365185164340.0835238965873-0.03033903423510.377139938057-0.02563933889770.260374894691-22.872593381814.4054981384-22.3040327934
111.04249013834-0.00484540685985-0.5804982314811.635828122590.5693936676972.17553040597-0.09053265371150.1763303535160.0666238719344-0.03240699662920.1279928499420.209837841252-0.00349128201814-0.188816306697-0.07542425681410.3023068395990.0150506296841-0.02204049444450.230821778440.02477447896790.279753507169-16.822448352740.449608319465.1947389718
124.2117293835-0.5019324743852.116469751242.335410681940.1049099396174.64692281470.177051617408-0.2824626314780.3599170959710.245820500644-0.276433329502-0.18015715109-0.3893853398280.2767254931250.08925963310040.320546042481-0.01872534800080.09773276313280.2789895031570.06067022271030.334649079981-17.741769584444.074038024497.5524046787
139.30827909999-1.841224262485.564387772694.35761623362-2.381463879727.26024333182-0.0363203185678-0.322875794232-0.376010236044-0.1750082465890.214777140550.5366892119480.700306457001-0.391950424269-0.01351209117810.26438564706-0.04139785188180.07418725563020.223214225767-0.04769395844960.379580122913-21.787975752916.371239048775.38624755
143.275722425210.2486324108010.5562801254943.37876489065-1.180512107373.36134609426-0.0121462151103-0.115672367131-0.451574467250.1327154589770.000959877954703-0.04903521026230.177383429659-0.104456508030.009942238213120.3127043313020.02940696419780.04967866450810.183871284787-0.004069467212670.267630922931-13.733329923519.995202026569.0147127866
150.966036032853-0.7687425882660.6554168668374.22426976745-3.153099596685.92897191836-0.136395384658-0.05515555233930.0108021384844-0.09689431795620.05825491863260.2189851401480.3064528052080.07330109405130.02065797666310.36192937698-0.02249193627980.06074366492490.271151451282-0.02015375321810.353182201974-17.340961515721.465972145171.1486844009
160.199712866935-0.308445783808-0.5567367629040.9823873257451.795518494433.28557411898-0.384890866114-0.3388891606140.06694354289240.3487415281970.4567979525030.3221018802850.73796024512-0.322655403180.03614747374250.5326269237110.05556170749670.1059472454620.3170358446060.1050335015610.292145037873-18.001171263818.13168577991.725251823
175.63887517077-2.94042675718-1.240848015942.881388834910.09360416280624.163725162170.180840325241-0.01994766445420.9841747058620.01086889838040.0533944554895-0.361212984329-0.354849687334-0.159305554602-0.1936255424090.404622736509-0.08121251531670.04972269029550.3271944363150.05460723365660.420505079513-24.419612560143.3923659913107.830392469
184.61434521928-3.08218160297-2.089734996222.998995246971.120534924133.42626625408-0.0692868667904-0.102826492775-0.2039021830290.130287018455-0.06370046067030.1742639680010.36133818567-0.01263974790570.1894076971550.258940646222-0.0486443817559-0.006283068608610.2146767196390.02650293194940.296713060631-29.083145255230.4990348221103.042028919
193.45491108075-1.20544014969-2.381212552662.520501970331.475930666023.614050249430.0660089768587-0.061180671153-0.19849987510.0736195791965-0.2397562996440.0797897451839-0.03432128394380.06887119985530.07377854038190.330768763128-0.0019918284161-0.001487923964120.2318105898080.05731096631440.201652604257-26.38318186831.8362841041106.029648565
202.401761190140.8089124814740.01790504615322.579942669280.3187582370841.412865759020.398881421602-0.9368556119940.2563646668230.173385166370.0684132191012-0.581395437650.1950070678490.612988268886-0.3099445432440.442660000232-0.00499766906949-0.01405433751080.862609863336-0.1805256619750.3383602016139.2675359011924.137658380748.8444730789
214.7635874428-0.7459795289310.4842959357644.30260060050.4253841793412.585106578040.225264972131-0.4929991257380.5055012828280.1821949460170.0918137889466-1.001109376-0.6405172834361.03845530246-0.2075125478180.581930464957-0.2468906753520.1728182923680.968179790621-0.1805439033010.70251264124118.421568398534.809167972847.3238256305
221.317313521030.100204600702-1.894934870180.288218733080.06346471476922.874332575350.592438931713-0.199784284864-0.04600802696010.01423491356430.130088429379-1.30154662583-0.2376418469990.724763562838-0.1324767919380.607322874968-0.3215401232280.08471538227491.87770791386-0.5822161442711.2954340978129.051931337634.54738259957.6911465497
238.031351586952.288588904941.961398607355.3741987041.218149751735.070673284040.0314751603150.3670808670581.01726947479-0.11383602450.291552687545-0.438341517656-0.5439103347330.617053369042-0.4280340763690.49397413035-0.03647226766830.05940866947720.360245673745-0.1435814587350.317685893857-0.57245517622833.437330455352.1272716747
245.26370324155-0.0407625069234-0.8207749870152.36655784483-0.03244975693472.689763339840.2096891245380.189173067373-0.8131468775670.025624140807-0.152111649701-0.1190624284510.3737368553560.604483183366-0.1474025805710.569825725380.116890316438-0.04764513226340.52771734992-0.07681442859840.2588142021812.2305181786319.765506916545.8100388324
254.101992957360.48745264707-0.693845822624.611123055360.2884467563583.20482390620.278854387195-0.409787978823-0.7162875331010.370329849436-0.263464832181-1.221710164440.7346563539041.68533438968-0.04081999154580.7321082495520.166587741306-0.1965693113771.32439308452-0.09409254993030.60651856348719.977868310515.515703452147.549683629
262.142599605310.2456775502450.005660781957950.330596513447-0.1438790779590.0861750522552-0.0920274165958-0.2349391031720.1306454515070.088831836919-0.0261249666829-0.4806850862840.05603801681850.04865950509740.02750187903240.3941740558590.5041657912150.00857551870182.04744439153-0.1862644863361.111716381734.657360316514.045869208244.9317991609
273.379116735182.01327704887-2.139112381223.426575583330.3328363772882.512939619090.34178230212-0.485890810421-0.895175909950.260409963865-0.214798876161-1.338109699580.2713466901880.628556781303-0.280902482960.4828605192150.194955993106-0.2191075630921.78575725232-0.3029600390371.0994866682827.047144326812.752280726636.464440883
285.07550471743-1.463426718921.028871020752.439954603090.3158490456133.891524487550.630733674672-0.302862915195-0.14776810476-0.106621778122-0.169845587551-0.3278820903010.7818895374250.457132343195-0.3624526834470.607750321780.1424565384090.07429704738880.388108666689-0.07887433338370.2905869585391.7216597002213.651288865339.2351681682
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 119 )HA1 - 1191 - 119
22chain 'H' and (resid 120 through 223 )HA120 - 223120 - 217
33chain 'L' and (resid 0 through 59 )LB0 - 591 - 60
44chain 'L' and (resid 60 through 73 )LB60 - 7361 - 74
55chain 'L' and (resid 74 through 100 )LB74 - 10075 - 101
66chain 'L' and (resid 101 through 111 )LB101 - 111102 - 112
77chain 'L' and (resid 112 through 126 )LB112 - 126113 - 127
88chain 'L' and (resid 127 through 161 )LB127 - 161128 - 162
99chain 'L' and (resid 162 through 172 )LB162 - 172163 - 173
1010chain 'L' and (resid 173 through 212 )LB173 - 212174 - 213
1111chain 'A' and (resid 1 through 119 )AC1 - 1191 - 119
1212chain 'A' and (resid 120 through 225 )AC120 - 225120 - 221
1313chain 'B' and (resid -1 through 16 )BD-1 - 161 - 18
1414chain 'B' and (resid 17 through 67 )BD17 - 6719 - 69
1515chain 'B' and (resid 68 through 99 )BD68 - 9970 - 101
1616chain 'B' and (resid 100 through 111 )BD100 - 111102 - 113
1717chain 'B' and (resid 112 through 126 )BD112 - 126114 - 128
1818chain 'B' and (resid 127 through 161 )BD127 - 161129 - 163
1919chain 'B' and (resid 162 through 210 )BD162 - 210164 - 212
2020chain 'C' and (resid 41 through 86 )CE41 - 861 - 46
2121chain 'C' and (resid 87 through 140 )CE87 - 14047 - 100
2222chain 'C' and (resid 141 through 170 )CE141 - 170101 - 127
2323chain 'C' and (resid 171 through 201 )CE171 - 201128 - 158
2424chain 'D' and (resid 40 through 75 )DF40 - 751 - 36
2525chain 'D' and (resid 76 through 140 )DF76 - 14037 - 98
2626chain 'D' and (resid 141 through 158 )DF141 - 15899 - 116
2727chain 'D' and (resid 159 through 169 )DF159 - 169117 - 127
2828chain 'D' and (resid 170 through 201 )DF170 - 201128 - 159

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